Fairfield Police Lt. Greg Hurlbut said during a press conference Monday that there was "garbage and spoiled food on the floor," as well as "animal and human feces and a large amount of debris making large amounts of the house unpassable."

Hurlbut said he believed the children had been home-schooled, but couldn't say if authorities had been contacted in the past about their living conditions.

Rogers claims the mess came from her tearing the house apart to look for her son in March. Lt. Hurlbut said officers found the boy sleeping under a bush in a neighbor's yard.

After investigators entered the home, Rogers' children were taken by child protective services and she was charged with child neglect.

During the following six weeks, investigators say the children started to open up about how Allen was treating them.

"The children described incidents of intentional abuse, puncture wounds, burns, bruising and injuries consistent with being shot with a pellet or BB gun," Hurlbut said.

"When the children were safe with other family members it came to light that there was significant abuse and incidents of torture," Chief Deputy District Attorney Sharon Henry said. "The children who were interviewed talked about the incidents, which went back several years."

Allegations in the criminal complaint date back to 2014, Henry said.

On Friday, officers arrested Allen, charging him with nine counts of felony torture and six counts of child abuse.

"That's why this is absolutely crazy," Rogers said of the children's father. "He was the nice guy. He was the one playing video games with them and I was telling them we need to clean up and do chores."

Rogers allowed KTXL to see the conditions inside her home but she claimed the mess was made by the police department when they arrested Allen.

"They tore up everything and I haven't had time to clean it because I've been back and forth to work. I work graveyard." Rogers said.

But officers say the conditions between their first visit in March and their second on Friday had not improved, although they did conduct a search of the home.

"So objects were obviously moved while conducting that search but that was not the basis for the charges regarding the environment the children were in though," Hurlbut said.

Allen is currently being held on $1.5 million bail at the Solano County Jail. Rogers was released after posting $10,000 bail following her March 31 arrest.